## [1] "C:/Users/jonat/OneDrive - University of Southern California/Github/macula_densa_scRNAseq"
options(future.globals.maxSize = 74 * 1024^3) # 55 GB
getOption("future.globals.maxSize") #59055800320
## [1] 79456894976

1 Load Raw Macula Densa .rds file

SO <- readRDS(here("outputs", "so_merge_raw.rds"))

head(SO@meta.data)
DimPlot(SO)

1.1 nFeatures, nCounts, and percent.mt

VlnPlot(SO, features = c("nFeature_RNA", "nCount_RNA", "percent.mt"), group.by = "orig.ident")

VlnPlot(SO, features = c("nFeature_RNA", "nCount_RNA", "percent.mt"), group.by = "sample")

FeaturePlot(SO, "nCount_RNA")

FeaturePlot(SO, "nFeature_RNA")

FeaturePlot(SO, "percent.mt")

1.2 Identify clusters

1.2.1 Cluster 0: MD1

1.2.2 Cluster 1: MD2

1.2.3 Cluster 2: MD: Activated (cFos)

1.2.4 Cluster 3: EC (Pecam1)

1.2.5 Cluster 4: Stroma (Vim)

1.2.6 Cluster 5: CD (Aqp2)

1.2.7 Cluster 6: IC (Kit)

1.2.8 Cluster 7: PT (Slc34a1)

SO.markers <- FindAllMarkers(SO, only.pos = TRUE)
SO.markers %>%
    group_by(cluster) %>%
    dplyr::filter(avg_log2FC > 1)
SO.markers %>%
    group_by(cluster) %>%
    dplyr::filter(avg_log2FC > 1) %>%
    slice_head(n = 5) %>%
    ungroup() -> top10
DoHeatmap(SO, features = top10$gene) + NoLegend()

markers.to.plot1 <- c("Lrp2",         # PT
                      "Slc5a12",      # PT-S1
                      "Slc13a3",      # PT-S2
                      "Slc16a9",      # PT-S3
                      "Havcr1",       # Injured PT
                      "Epha7",        # dTL
                      "Cryab",        # dTL
                      "Cdh13",        # dTL1
                      "Slc14a2",      # dTL2
                      "Slc12a1",      # TAL
                      "Umod",         # TAL, DCT1
                      "Egf",          # TAL, DCT1,
                      "Cldn10",       # TAL
                      "Cldn16",       # TAL
                      "Nos1",         # MD
                      "Slc12a3",      # DCT
                      "Pvalb",        # DCT1
                      "Slc8a1",       # DCT2, CNT
                      "Aqp2",         # PC
                      "Slc4a1",       # IC-A
                      "Slc26a4",      # IC-B
                      "Nphs1",        # Podo
                      "Ncam1",        # PEC
                      "Flt1",         # Endo
                      "Emcn",         # Glom Endo
                      "Kdr",          # Capillary Endo
                      "Pdgfrb",       # Perivascular
                      "Pdgfra",       # Fib
                      "Piezo2",       # Mesangial
                      "Acta2",        # Mural
                      "Ptprc",        # Immune
                      "Cd74",         # Macrophage
                      "Skap1",        # B/T Cells 
                      "Upk1b",        # Uro
                      "Top2a"         # Proliferation
)
                      
DotPlot(SO,
features = markers.to.plot1,
dot.scale = 8,
dot.min = 0,
scale.max = 100,
scale.min = 0,
col.min = -2.5,
col.max = 2.5)+
coord_flip()

1.3 Check FeaturePlot/VlnPlot

df_5 <- FindMarkers(SO, ident.1 = 5, min.pct = 0.25)
df_5_rownames <- rownames(df_5)
df_5_rownames
##    [1] "9230102O04Rik" "A930017K11Rik" "Apela"         "Aqp2"         
##    [5] "Aqp3"          "Calb1"         "Cav1"          "Defb2"        
##    [9] "Depdc7"        "Ednrb"         "Emx1"          "Fxyd4"        
##   [13] "Gata2"         "Gata3"         "Iqgap2"        "Kcne1"        
##   [17] "Mpped2"        "Npnt"          "Pde3b"         "Pgam2"        
##   [21] "Phactr1"       "Ptgfr"         "Rhcg"          "Scnn1b"       
##   [25] "Scnn1g"        "Spink8"        "St6gal1"       "Stc1"         
##   [29] "Tbx2"          "Tmem45b"       "Trpv5"         "Avpr2"        
##   [33] "Trpv4"         "Tmem229a"      "Atp2b2"        "Ptgs1"        
##   [37] "Srcin1"        "Slc2a9"        "A4galt"        "Adm"          
##   [41] "Kcnj10"        "Cdc42ep1"      "Rasd1"         "Cryab"        
##   [45] "Sgk1"          "Ccnd1"         "Tacstd2"       "Dab2"         
##   [49] "Slc8a1"        "Gm44120"       "Angpt1"        "Tmem52b"      
##   [53] "Hsd11b2"       "Hspg2"         "Adh1"          "Kcnq1"        
##   [57] "Smtn"          "Itpkb"         "Ddah1"         "Itga2b"       
##   [61] "Cav2"          "Rhbg"          "Gchfr"         "Csrp2"        
##   [65] "Hdac7"         "Kitl"          "Itpr2"         "Plcd3"        
##   [69] "Rap1gap"       "Phlda1"        "Krt7"          "Hhatl"        
##   [73] "Tspan1"        "Slc6a6"        "Cox7a1"        "Rnf186"       
##   [77] "Gprc5b"        "Ntn4"          "1110019B22Rik" "St6galnac2"   
##   [81] "Rec8"          "Grb14"         "Cavin2"        "Tpd52l1"      
##   [85] "Gm43305"       "Slc12a1"       "Sfrp1"         "Nuak2"        
##   [89] "Defb1"         "Igfbp7"        "Sec14l1"       "4930550C14Rik"
##   [93] "Col27a1"       "Il17re"        "Irx1"          "Emb"          
##   [97] "Lhx1"          "Cldn4"         "Car15"         "Etnk1"        
##  [101] "Nudt4"         "Pik3r1"        "Zfand5"        "Cd63"         
##  [105] "Zfp503"        "Slc5a1"        "Cox7b"         "Eprn"         
##  [109] "Robo2"         "Irx2"          "Bmp3"          "Mgst1"        
##  [113] "Abca13"        "Scd2"          "Slc44a3"       "Cldn10"       
##  [117] "Aebp1"         "Gm10053"       "Gm42031"       "Ftl1"         
##  [121] "Chchd10"       "Ctsc"          "Prdx5"         "Tnfaip8"      
##  [125] "Gm22133"       "Slc25a5"       "Apoe"          "Cyba"         
##  [129] "Uqcrb"         "Itprid2"       "Plcl1"         "Serinc3"      
##  [133] "Pcolce"        "L1cam"         "Sptbn2"        "Gm49980"      
##  [137] "Cox6a1"        "Thbs1"         "Cox6c"         "Gapdh"        
##  [141] "Aif1l"         "Pdzk1ip1"      "Camk2d"        "Osbpl1a"      
##  [145] "Cox5a"         "Exph5"         "Ttc36"         "Pth1r"        
##  [149] "Pamr1"         "Ndufa4"        "Ramp3"         "Cox5b"        
##  [153] "Herpud1"       "Wwc2"          "Ltc4s"         "Esd"          
##  [157] "Ndufc1"        "Atp5h"         "Atp5o"         "Sh3bgrl3"     
##  [161] "Enpp1"         "Peli2"         "Scnn1a"        "Uqcrq"        
##  [165] "Ppp1r1a"       "Atp5j2"        "Col4a1"        "Eno1"         
##  [169] "Gm47708"       "Nadk2"         "Pappa2"        "Apoo"         
##  [173] "Atp5mpl"       "Ndufb1-ps"     "Mfge8"         "Flvcr1"       
##  [177] "Ndufa5"        "Cdk14"         "Ranbp3l"       "Cyb5a"        
##  [181] "Atp5k"         "Cycs"          "Ces1d"         "Efhd1"        
##  [185] "Cnn3"          "Sdc4"          "Uqcr11"        "H3f3b"        
##  [189] "Mapt"          "Ctsb"          "Nos1"          "Cd47"         
##  [193] "Uqcr10"        "Mt2"           "Atp5g3"        "Enpp2"        
##  [197] "Atp5md"        "Rps5"          "Smim4"         "S100g"        
##  [201] "Cth"           "Pacsin2"       "mt-Cytb"       "Atp5g1"       
##  [205] "Atp5j"         "Mt1"           "mt-Rnr1"       "Avpr1a"       
##  [209] "Ppargc1a"      "Lix1"          "Atp5e"         "Neat1"        
##  [213] "Tfrc"          "Cdkn1c"        "Fam241a"       "Ndufa1"       
##  [217] "Plcb1"         "Fxyd2"         "Cox7a2"        "mt-Rnr2"      
##  [221] "Cdo1"          "Fzd4"          "Snn"           "Ndrg1"        
##  [225] "Fam3c"         "Cacna1d"       "Lgmn"          "Pde10a"       
##  [229] "Sgms2"         "Bex1"          "Hes1"          "Ptma"         
##  [233] "Tmem176b"      "Col4a3"        "Itga4"         "Paqr5"        
##  [237] "Idh2"          "Bex4"          "Ablim1"        "Aldoa"        
##  [241] "Napsa"         "Cox8a"         "Gm28437"       "Car4"         
##  [245] "Tfap2b"        "Oxct1"         "Rps3"          "Scarf2"       
##  [249] "Ndufb6"        "Slit2"         "Tmem176a"      "Car8"         
##  [253] "Tshr"          "Cwh43"         "Ctsz"          "Clic1"        
##  [257] "Por"           "Hif1a"         "Tmem221"       "Ppp2r3a"      
##  [261] "Epcam"         "Degs2"         "Tspan18"       "Erbb4"        
##  [265] "Tmem72"        "Cst3"          "Ahnak"         "Cox7c"        
##  [269] "Plekha1"       "Gm10108"       "Ptger3"        "Oat"          
##  [273] "Sytl2"         "Asph"          "Kl"            "Aco2"         
##  [277] "Gm10221"       "Shd"           "Cox6b1"        "Myef2"        
##  [281] "Tmsb10"        "Ndufa3"        "Hspa1b"        "Tmsb4x"       
##  [285] "Rpl9"          "Ndufa2"        "Uqcrh"         "Ndufa6"       
##  [289] "Fam53b"        "Mfsd4b1"       "Bcam"          "Gstt1"        
##  [293] "Rps8"          "Rps21"         "Zcchc18"       "Ndufv3"       
##  [297] "Ptges"         "Sqstm1"        "Pla2g7"        "Lmo1"         
##  [301] "Uroc1"         "Rpl3"          "Myo10"         "mt-Nd4l"      
##  [305] "Atp2a2"        "Col18a1"       "Rnf152"        "Rpl7"         
##  [309] "Clcnkb"        "Srpk2"         "Smpdl3a"       "Gm12337"      
##  [313] "Rps14"         "Pantr1"        "Slc31a1"       "Atp5pb"       
##  [317] "Rassf6"        "Rrbp1"         "Sh2d4a"        "Gstm1"        
##  [321] "Selenom"       "Tmem59"        "H2-D1"         "Atp6v0b"      
##  [325] "S100a1"        "Pkig"          "Mgll"          "Wwc1"         
##  [329] "Gm3379"        "Ucp2"          "Mrpl42"        "Iscu"         
##  [333] "H2bc4"         "D630024D03Rik" "Acsl4"         "Idh3a"        
##  [337] "Pgk1"          "Fth1"          "Epn3"          "Ndufb10"      
##  [341] "Atp5b"         "Atp2b1"        "Rps7"          "Ndufa13"      
##  [345] "Thsd4"         "Rps3a1"        "Gnas"          "S100a11"      
##  [349] "Tecr"          "Bex3"          "Tbck"          "Rhoc"         
##  [353] "Hspa1a"        "S100a10"       "Slc24a5"       "Hoxb7"        
##  [357] "Nrp1"          "Cldn16"        "Kcnk1"         "mt-Nd2"       
##  [361] "Clint1"        "Gm10925"       "Rps24"         "Hoxb4"        
##  [365] "Gm4735"        "Zmiz1"         "Gm9732"        "Sptbn1"       
##  [369] "Pbx3"          "Npc2"          "Rps9"          "Ipcef1"       
##  [373] "Kng2"          "Srrm2"         "Cnbp"          "Rgs2"         
##  [377] "Tmem64"        "Atp2b4"        "Acat1"         "Sox4"         
##  [381] "Higd1a"        "Gm12338"       "Rps4x"         "Atp1b1"       
##  [385] "Glud1"         "Ftl1-ps1"      "Bola3"         "Ccdc80"       
##  [389] "Emp2"          "Fam174b"       "Pgp"           "Cyb5b"        
##  [393] "mt-Nd1"        "Tcf4"          "Bmpr1b"        "Tpi1"         
##  [397] "Tmem158"       "Stk32b"        "Klhdc7a"       "Fahd1"        
##  [401] "Bst2"          "Ndufa8"        "Bag1"          "Zbtb20"       
##  [405] "Dock8"         "Gga2"          "B830017H08Rik" "Peg3"         
##  [409] "Gclc"          "Uqcrfs1"       "C77080"        "Spp1"         
##  [413] "Fzd7"          "Pkm"           "Tagln2"        "Paip2"        
##  [417] "Gnai1"         "Ndufv2"        "Metrnl"        "Reep5"        
##  [421] "Smco4"         "Usp2"          "Pigp"          "Dusp9"        
##  [425] "Nipal2"        "Cdkl1"         "Got1"          "Rpl9-ps7"     
##  [429] "Fras1"         "Cystm1"        "Ier3"          "Ndufb5"       
##  [433] "Tspan33"       "Lurap1"        "Ndufa12"       "Ndufa11"      
##  [437] "Ndufb11"       "Zfp36l1"       "Dbndd2"        "Map1lc3a"     
##  [441] "Rpl17-ps3"     "Hpcal1"        "Sdc2"          "Wsb1"         
##  [445] "Muc1"          "Rps16"         "Stx7"          "Gas5"         
##  [449] "Gcgr"          "Mrpl36"        "Nsg2"          "Bcl2"         
##  [453] "Rpl30"         "Glis2"         "Baiap2"        "Mcub"         
##  [457] "Tspan15"       "Vdac1"         "Rpl8"          "Hoxc6"        
##  [461] "Tbxas1"        "Sod2"          "Eef1b2"        "Prkd1"        
##  [465] "4930581F22Rik" "Akr1b8"        "Dctd"          "Acss1"        
##  [469] "Ndufaf4"       "Chchd2"        "Rpl18a"        "Ndufb2"       
##  [473] "Gabarapl1"     "Ndst4"         "Dapk1"         "Ndufc2"       
##  [477] "Ank3"          "Tspan12"       "Slc25a17"      "Gm28438"      
##  [481] "Slc50a1"       "Cox20"         "Ndufb7"        "Ctsl"         
##  [485] "Prom1"         "Rnf145"        "Gm15427"       "Nenf"         
##  [489] "Pla2g4a"       "Hoxc9"         "B3gnt2"        "Gm28661"      
##  [493] "Srgap1"        "Mdh2"          "Ppp1r14b"      "Stard4"       
##  [497] "Atp5a1"        "Ninl"          "Ripor1"        "BC064078"     
##  [501] "Rps15a"        "Kank1"         "Nampt"         "Mrps21"       
##  [505] "Ppm1h"         "Rpl34"         "Klk1b4"        "Fmc1"         
##  [509] "Slc3a2"        "Rps15"         "Vegfa"         "Arhgap24"     
##  [513] "2300009A05Rik" "Pde4d"         "Chpt1"         "Gal3st1"      
##  [517] "Rps2"          "Jun"           "Lrpap1"        "Pappa"        
##  [521] "Nr3c2"         "Trim2"         "mt-Nd4"        "Mfsd4a"       
##  [525] "Ube2h"         "Mgst3"         "Fut8"          "Ldhb"         
##  [529] "Micos10"       "Cebpd"         "Thoc2l"        "St3gal4"      
##  [533] "Kctd1"         "Plcxd3"        "Lmna"          "Tpt1"         
##  [537] "Utrn"          "Hoxc8"         "Rps27a"        "Slc29a1"      
##  [541] "Naca"          "B2m"           "Gdf11"         "Ndfip1"       
##  [545] "Nudt19"        "Selenok"       "Syne1"         "Cbx5"         
##  [549] "Eef1d"         "Ly6e"          "Atp5l"         "Atp6v0e"      
##  [553] "Tmed6"         "Npm1"          "Tubb2a"        "Sema6a"       
##  [557] "Ttc14"         "Hsp90ab1"      "Sptlc2"        "Enpp4"        
##  [561] "Cgnl1"         "Ksr2"          "Hoxb2"         "Ass1"         
##  [565] "Rps13"         "Arid5b"        "Selenow"       "Gm14414"      
##  [569] "Atp4a"         "Rps10"         "Aard"          "Gm5526"       
##  [573] "Dynlt1f"       "Hnrnpa0"       "Sema5a"        "Spcs2"        
##  [577] "Rpsa-ps2"      "Bcl7a"         "Ptgs2"         "Akap13"       
##  [581] "Hoxb9"         "Micall1"       "Mettl7a1"      "Snrnp70"      
##  [585] "Aig1"          "Rps3a2"        "Olfm1"         "Anxa11"       
##  [589] "Glis3"         "Ndufs5-ps"     "Cdc42bpa"      "Gm24447"      
##  [593] "Hexa"          "Rpl6l"         "Atp5c1"        "Dbi"          
##  [597] "Hoxb5os"       "Myh10"         "Fau"           "Ermp1"        
##  [601] "Saraf"         "Etv1"          "Atp6v1f"       "Enox1"        
##  [605] "Frmd4a"        "Gpc3"          "Erp29"         "Cdh6"         
##  [609] "Gm45716"       "Cog7"          "Fuom"          "Smdt1"        
##  [613] "Gm6136"        "Esrra"         "Mcee"          "Rps19"        
##  [617] "Cox4i1"        "Ptpn3"         "Slc9a3r1"      "Serpinb1a"    
##  [621] "Rtn4"          "Srrm1"         "Mvb12a"        "Bcl2l1"       
##  [625] "Rps16-ps2"     "Rpl12"         "Ezr"           "Rpl4"         
##  [629] "Gm7206"        "Id4"           "Rps20"         "Setd5"        
##  [633] "Klf9"          "Prss23"        "Tnfrsf21"      "Pnisr"        
##  [637] "Ndufb4c"       "Baiap2l2"      "Shmt1"         "Dynlt1a"      
##  [641] "Tcf24"         "Tsn"           "Fus"           "Rabac1"       
##  [645] "Mal"           "Ddah2"         "Tle4"          "Rack1"        
##  [649] "Ctnna1"        "Hoxb6"         "Rpl27a"        "F11r"         
##  [653] "Itm2c"         "Etfa"          "Snw1"          "Mtdh"         
##  [657] "Rps12"         "Thap4"         "Rpl10-ps3"     "Gm12251"      
##  [661] "Plscr2"        "Mtus1"         "Sf3b1"         "Mtfp1"        
##  [665] "Srpr"          "Tspan7"        "Gm26377"       "Rps18"        
##  [669] "6330403K07Rik" "Tenm2"         "Serpinb6a"     "Gm4045"       
##  [673] "Defb42"        "Tmed9"         "Rpl10a-ps1"    "Cirbp"        
##  [677] "Slc39a8"       "Rpl5"          "Eif3f"         "Gm4332"       
##  [681] "Ddt"           "Creg1"         "Aimp1"         "Auts2"        
##  [685] "Nr3c1"         "Kifc3"         "Diaph2"        "Ndufa10"      
##  [689] "Rpl10"         "Hnrnpa3"       "Sdhc"          "Jund"         
##  [693] "Rps27"         "Pkdcc"         "Gpx6"          "Mcrip2"       
##  [697] "Rmdn3"         "Cldn7"         "Serpinh1"      "Ddrgk1"       
##  [701] "Sorl1"         "Gaa"           "Lcorl"         "Rmnd5a"       
##  [705] "Cpt1a"         "Atp5d"         "Sult1c2"       "Hk1"          
##  [709] "Ptprf"         "Tusc3"         "Ssbp2"         "Notch2"       
##  [713] "Luc7l2"        "Mal2"          "Trmt112"       "Gm9790"       
##  [717] "Gm20554"       "Tln2"          "Mmp14"         "Fam162a"      
##  [721] "Gm11353"       "C2cd5"         "Clu"           "Slc25a35"     
##  [725] "Nop10"         "Tmem116"       "Ddit4l"        "Srp14"        
##  [729] "Pdk3"          "Dynll1"        "Ctsh"          "Ndufb8"       
##  [733] "Thra"          "Rps23"         "Gm4294"        "Cldn8"        
##  [737] "Mdh1"          "Cab39l"        "Slc25a3"       "Mia2"         
##  [741] "Kidins220"     "Gm48582"       "Pdgfa"         "Dmxl1"        
##  [745] "Me3"           "Atp9a"         "Sema4a"        "Usp50"        
##  [749] "Tnfaip2"       "Ypel2"         "Rsrp1"         "Ubb"          
##  [753] "Rnasek"        "Gm5436"        "Sdcbp"         "Cd9"          
##  [757] "Gstp-ps"       "Hpn"           "Riok3"         "Ndufs8"       
##  [761] "Smc1a"         "Capns1"        "Tmed3"         "Pigq"         
##  [765] "Tmem47"        "Nsmce3"        "Rnf128"        "Minpp1"       
##  [769] "Slc16a7"       "H2-K1"         "Kdm1b"         "Mrps36"       
##  [773] "Gm44386"       "Celsr2"        "U2surp"        "Coa3"         
##  [777] "Nfix"          "Ndufa12-ps"    "Hadh"          "Slc9a2"       
##  [781] "Ndufb3"        "Gm2962"        "Hnrnpu"        "Vps13c"       
##  [785] "Gm15590"       "Gnb4"          "Rpl18-ps2"     "Gm3362"       
##  [789] "Mtln"          "Sec62"         "Rpl23"         "Srsf7"        
##  [793] "Cspp1"         "Trabd2b"       "Eps8"          "Prrc2c"       
##  [797] "Ifi27"         "Rpsa"          "Hoxc10"        "Inpp5a"       
##  [801] "AI838599"      "Slc35g1"       "Gm13436"       "Bptf"         
##  [805] "Net1"          "Aff1"          "Clcn5"         "Bod1l"        
##  [809] "Bcat2"         "Rpl11"         "Iah1"          "Tmbim6"       
##  [813] "Lamp2"         "Sh3bp5"        "Rdm1"          "4921524J17Rik"
##  [817] "Dcdc2a"        "Tbc1d1"        "Cx3cl1"        "Pdpn"         
##  [821] "Ncam1"         "Rpl22"         "Eef1g"         "Rpl29"        
##  [825] "Prpf4b"        "Mccc1"         "Hnrnpdl"       "Rpl15-ps2"    
##  [829] "Klhl3"         "Cnpy2"         "Kcnj16"        "Cited4"       
##  [833] "Mif"           "Adamtsl2"      "Rbm39"         "Gm14539"      
##  [837] "Sri"           "Gars"          "Hyi"           "C1qtnf4"      
##  [841] "Smim24"        "Syne2"         "Mpp6"          "Tmtc4"        
##  [845] "Atl2"          "Cd81"          "Ash1l"         "Tmed4"        
##  [849] "Stx16"         "Rpl14"         "Tmem254c"      "Mapk13"       
##  [853] "Slc25a4"       "Rpl26"         "Atraid"        "Ncor1"        
##  [857] "Atp6v1a"       "ccdc198"       "Etfb"          "Ly6a"         
##  [861] "Bex2"          "Arl6"          "Smim5"         "Srsf11"       
##  [865] "Stk26"         "Cers4"         "Gm13340"       "Hmgn5"        
##  [869] "Ghitm"         "Knop1"         "Hadhb"         "Itgav"        
##  [873] "Nhs"           "Tnrc6c"        "Chd2"          "Ing2"         
##  [877] "Serinc1"       "Nono"          "Trps1"         "Csrp1"        
##  [881] "Dhrs4"         "Extl1"         "Hoxb3"         "Wnt10a"       
##  [885] "Mme"           "Tsc22d2"       "Srsf3"         "Gm10039"      
##  [889] "Hebp1"         "Gm10774"       "Cnot6l"        "Myo18a"       
##  [893] "Ppp3ca"        "Nudt22"        "Gstk1"         "Pura"         
##  [897] "Stk25"         "Cyp2j11"       "Ptk7"          "Rbm3"         
##  [901] "Pou3f3"        "Rtn3"          "Pdzrn4"        "Batf3"        
##  [905] "Gm3511"        "Mtx2"          "Luzp1"         "Grk3"         
##  [909] "Fbxo44"        "6430548M08Rik" "Rps19-ps2"     "Hoxd3os1"     
##  [913] "Sash1"         "Cryz"          "Cdhr5"         "Arhgef12"     
##  [917] "Prelid2"       "Ethe1"         "Rplp1"         "Arnt2"        
##  [921] "Itgb1"         "Vkorc1"        "Rpl10a"        "Ckap4"        
##  [925] "Camk2n1"       "4632427E13Rik" "Ppm1j"         "Gas6"         
##  [929] "Hnrnpd"        "Rpl19"         "Hnrnph1"       "Gm29216"      
##  [933] "Acin1"         "Dld"           "Tmem141"       "Timp3"        
##  [937] "Ssr4"          "Pfkp"          "Rpl17"         "Uhrf2"        
##  [941] "Nipsnap1"      "Rps6-ps1"      "Gls"           "Ppfibp1"      
##  [945] "Dhcr24"        "Gpm6b"         "Ddost"         "Csnk1a1"      
##  [949] "Dop1b"         "Ldha"          "Rpl18"         "Rnpep"        
##  [953] "Acss3"         "Sdhd"          "Tubb5"         "Fgf9"         
##  [957] "Zfp326"        "Hnrnpk"        "Eef1a1"        "Nsd1"         
##  [961] "Rps26"         "Vash2"         "Itpr1"         "Micos13"      
##  [965] "Tpp1"          "Prnp"          "Kng1"          "Nsmce4a"      
##  [969] "Cers6"         "Eif1"          "Atp6ap1"       "Nrip1"        
##  [973] "Stim2"         "Hint2"         "Smarca2"       "Mafg"         
##  [977] "Sema3c"        "Bhlhe40"       "Nhsl2"         "Abca3"        
##  [981] "Rock1"         "Sv2a"          "Ctsf"          "Ptprd"        
##  [985] "Srsf5"         "Uqcrc2"        "Tmem50a"       "Nedd4l"       
##  [989] "Rpn2"          "Myo1b"         "Ndufs5"        "Cabcoco1"     
##  [993] "Psmd4"         "Dusp14"        "Ube2d3"        "Clta"         
##  [997] "Tmem254b"      "Rabgef1"       "Trim47"        "Plin3"        
## [1001] "Ccdc141"       "Tnrc6a"        "Nr2f2"         "Atf7ip"       
## [1005] "F2rl1"         "Eva1a"         "Lmo7"          "Emc7"         
## [1009] "Mfsd4b3-ps"    "Rbm47"         "Ran"           "Trp53i13"     
## [1013] "Mmd"           "Fnbp1l"        "Txnip"         "Matr3"        
## [1017] "Gabarap"       "Gm9349"        "Rps27l"        "Vps37d"       
## [1021] "Sgms1"         "Rpl37"         "Birc2"         "Cables1"      
## [1025] "Luzp2"         "Ywhah"         "Srsf1"         "Glmp"         
## [1029] "Rdx"           "Wdr72"         "Ppdpf"         "Trim35"       
## [1033] "Iqgap1"        "Trim44"        "Dnah12"        "Sfn"          
## [1037] "Tmem238"       "Hipk2"         "Tgoln1"        "Gm28911"      
## [1041] "H2az2"         "Laptm4b"       "Gigyf2"        "Atrx"         
## [1045] "Mindy2"        "Dbt"           "Msi2"          "Cmc2"         
## [1049] "Trim7"         "Crim1"         "Tle1"          "Umod"         
## [1053] "Pdia3"         "Mgat4a"        "Cetn3"         "Cldnd1"       
## [1057] "Hmgb2"         "Rchy1"         "Pde1a"         "Gcnt2"        
## [1061] "Morf4l1"       "Dhrs7"         "Ptprj"         "Rpl23a"       
## [1065] "Prkar1a"       "Fads1"         "Os9"           "Canx"         
## [1069] "Car12"         "Gm8971"        "Atp11a"        "Gnb2"         
## [1073] "Rpl37a"        "Ccnt2"         "Rsrc2"         "Ergic3"       
## [1077] "Rplp0"         "Gm7536"        "Mxd4"          "Hivep2"       
## [1081] "Slc2a1"        "Klk1b5"        "Rps8-ps1"      "Rab20"        
## [1085] "Rbm25"         "Fam107b"       "Anxa5"         "Rpl7a"        
## [1089] "Tle5"          "Osbpl6"        "Selenop"       "Ndufb4"       
## [1093] "Hoxd11"        "Ptbp3"         "Cdc42se2"      "Psip1"        
## [1097] "Gm9843"        "Gpi1"          "Aamp"          "Pla2g12a"     
## [1101] "Acot9"         "Hint3"         "Zfp950"        "Bicc1"        
## [1105] "Jarid2"        "Srebf2"        "Sms"           "Pdha1"        
## [1109] "Snx2"          "Slc1a3"        "Vgll4"         "Fh1"          
## [1113] "Map1lc3b"      "Apmap"         "Prxl2a"        "Vdac2"        
## [1117] "1110008P14Rik" "Nktr"          "Rpl32"         "Lmbrd1"       
## [1121] "Rsu1"          "Atp6v1g1"      "Gm2830"        "Gm13226"      
## [1125] "Hnrnpa2b1"     "Limch1"        "Prrc2b"        "Gm45847"      
## [1129] "Pls3"          "Tm2d1"         "Itga1"         "Wdfy3"        
## [1133] "Aifm1"         "Grina"         "Gm46209"       "Slc25a12"     
## [1137] "Tm7sf3"        "Psmb1"         "Atp6v1c2"      "Jak1"         
## [1141] "Slc7a4"        "Morn2"         "Nfic"          "Gpx4-ps2"     
## [1145] "Glo1"          "Malat1"        "Cyp39a1"       "Efcab14"      
## [1149] "Kmt2a"         "Psme1"         "Kdsr"          "Dpysl2"       
## [1153] "Tax1bp1"       "Ndufs1"        "Dlat"          "Ints6l"       
## [1157] "2610528J11Rik" "Ccdc107"       "Tia1"          "Sfpq"         
## [1161] "Myh9"          "Pabpc1"        "Ogfrl1"        "Ik"           
## [1165] "Clk1"          "Sgpp1"         "Uqcrc1"        "Purb"         
## [1169] "Tmed1"         "Mettl26"       "Rex1bd"        "Gstm2"        
## [1173] "Lrp6"          "Ptprg"         "Zranb2"        "Mafb"         
## [1177] "Ormdl3"        "Slc15a2"       "Rps27rt"       "Akap9"        
## [1181] "Ndufab1"       "Hnrnpl"        "Dock1"         "Ano6"         
## [1185] "Megf9"         "Gna11"         "Dab2ip"        "Dtymk"        
## [1189] "Grcc10"        "Rpgrip1"       "Gm8451"        "Rpl28"        
## [1193] "Crebbp"        "Dpyd"          "Acot1"         "Sgcb"         
## [1197] "Acadsb"        "Gsk3b"         "Lamp1"         "Rpl13-ps3"    
## [1201] "Cttnbp2"       "Serbp1"        "Txndc5"        "Dgat2"        
## [1205] "Frk"           "Eif6"          "Dip2c"         "Vav3"         
## [1209] "Fbxo6"         "Rnf187"        "Cyfip2"        "Cryl1"        
## [1213] "Eif5a"         "Ythdc1"        "Tmbim1"        "Ube2a"        
## [1217] "Pi4ka"         "Orai1"         "Calr"          "Ip6k2"        
## [1221] "Raly"          "Magi2"         "Map3k3"        "Syt11"        
## [1225] "Klf13"         "Eif3i"         "Higd2a"        "Abhd6"        
## [1229] "Arhgef18"      "Ddx50"         "Ywhaq"         "Id3"          
## [1233] "Ptpn18"        "Elob"          "Tmpo"          "Pnrc1"        
## [1237] "Btf3"          "Efemp1"        "Shfl"          "Bclaf1"       
## [1241] "Eif3k"         "Cebpb"         "Rora"          "Ube2b"        
## [1245] "Ldhb-ps"       "Tbrg1"         "Sypl"          "Tmx1"         
## [1249] "Gm9616"        "Col4a3bp"      "Macroh2a1"     "Olfm4"        
## [1253] "Ctsa"          "Ppp1r2"        "Leng8"         "Luc7l3"       
## [1257] "Wee1"          "Nucb1"         "Dync1h1"       "Pdlim5"       
## [1261] "Ralbp1"        "Pgrmc1"        "Kmt2e"         "Gm11914"      
## [1265] "Cox17"         "Eif3h"         "Ndufs4"        "Slc16a11"     
## [1269] "Sfxn1"         "Acsl3"         "Erg28"         "Cachd1"       
## [1273] "Tmem222"       "Csad"          "Wasl"          "Oard1"        
## [1277] "Sec11c"        "C1qtnf12"      "Gnptg"         "Sgpl1"        
## [1281] "Lpar6"         "Mrpl57"        "Vegfb"         "Itgb5"        
## [1285] "Mecom"         "Pold4"         "Prdx4"         "Gstm5"        
## [1289] "Fndc3a"        "Slc16a10"      "Gprasp1"       "Tma7"         
## [1293] "Wfdc2"         "Spcs1"         "Ktn1"          "Dcps"         
## [1297] "Letm2"         "Lman1"         "Thrap3"        "Coq7"         
## [1301] "Pten"          "Maged1"        "Rpl14-ps1"     "Krcc1"        
## [1305] "Slco4a1"       "Crebzf"        "Selenbp1"      "Cebpa"        
## [1309] "Kif5b"         "Ppa2"          "Trim24"        "Arhgef28"     
## [1313] "Xiap"          "Slirp"         "Nifk"          "Acadm"        
## [1317] "Degs1"         "Phf3"          "Cmtm8"         "Rab11fip2"    
## [1321] "Ndufs3"        "Tardbp"        "Psma7"         "Crem"         
## [1325] "Erbb3"         "Rsbn1"         "Yipf1"         "Rps23-ps1"    
## [1329] "Gm10177"       "Gng5"          "Zfp467"        "Sec31a"       
## [1333] "Asah1"         "Hoxa9"         "Irf2bp2"       "Exosc3"       
## [1337] "Rbbp6"         "Gm8355"        "Bnip3"         "Oaz1"         
## [1341] "Fermt2"        "Fuca1"         "Pafah1b3"      "Gm11539"      
## [1345] "Mecp2"         "Spag9"         "Eif4a2"        "Arid4b"       
## [1349] "Snhg20"        "Cox5b-ps"      "Tceal8"        "Cd151"        
## [1353] "Mrpl12"        "Pdia6"         "Ahcyl2"        "Sorbs2"       
## [1357] "Rpl22l1"       "Yif1a"         "Casr"          "Sdf2"         
## [1361] "Nedd4"         "Pmepa1"        "Eri3"          "Dlgap4"       
## [1365] "Vps25"         "Serinc2"       "Bag4"          "Tmem9"        
## [1369] "Sbds"          "Pfn2"          "Hivep1"        "Rbpms"        
## [1373] "Mycbp2"        "H2aj"          "Hspe1"         "Timp2"        
## [1377] "Dusp23"        "Pcdhgc4"       "Marf1"         "Hnrnph3"      
## [1381] "Maml3"         "Hspa8"         "Thoc1"         "Rbmx"         
## [1385] "Cox7a2l"       "Usp22"         "Zfp266"        "Sec61g"       
## [1389] "Csde1"         "R3hdm2"        "Rxrb"          "Nucks1"       
## [1393] "Mrpl51"        "Mydgf"         "Dtnbp1"        "Cdc25b"       
## [1397] "Gcc2"          "Pabpn1"        "Cnot4"         "Gm15459"      
## [1401] "Smg6"          "Calm1"         "Adam15"        "Rbm5"         
## [1405] "Atxn1"         "Slc38a10"      "Mef2a"         "Pbx1"         
## [1409] "Cyc1"          "Pygl"          "Smim6"         "Dctn3"        
## [1413] "Coq9"          "Pitpna"        "Snrpb"         "Csf2ra"       
## [1417] "Anp32e"        "Sucla2"        "Hnf1b"         "Gm8430"       
## [1421] "Rcbtb2"        "Pnn"           "Dnajc3"        "Ttc3"         
## [1425] "Top1"          "Rnd3"          "Plpp2"         "Fam204a"      
## [1429] "Rpl6"          "Cs"            "Gadd45g"       "Pdhb"         
## [1433] "Psmd7"         "Frg1"          "Casp6"         "Nptn"         
## [1437] "Chd3"          "Myo6"          "Atp6v0a4"      "Nme3"         
## [1441] "Actr10"        "4932438A13Rik" "Nol7"          "Macf1"        
## [1445] "Rprd2"         "Hibadh"        "Gng12"         "Oip5os1"      
## [1449] "Rpl13"         "Ccni"          "Ptpra"         "Egf"          
## [1453] "Ddx24"         "Abhd2"         "Sgta"          "Rpl13a"       
## [1457] "Tufm"          "Gm10232"       "Rell1"         "Ache"         
## [1461] "Las1l"         "Kif16b"        "Scin"          "Btbd3"        
## [1465] "Brd2"          "Ggh"           "Dbnl"          "Lsm4"         
## [1469] "Mkln1"         "Zadh2"         "Izumo4"        "Tm9sf2"       
## [1473] "Tmem191c"      "Immt"          "Zfr"           "Nsun7"        
## [1477] "Pink1"         "Sestd1"        "Usp24"         "Plet1"        
## [1481] "Arhgdia"       "Tcf7l2"        "Tspan3"        "Lamb1"        
## [1485] "Rpl36a-ps3"    "Prdx3"         "Nipbl"         "Rictor"       
## [1489] "Arpc1a"        "Sf3b5"         "Arfgef3"       "Ndfip2"       
## [1493] "Cpsf6"         "Hoxb8"         "Fam174a"       "Zfp644"       
## [1497] "Spopl"         "Rtl8a"         "Mfsd1"         "Kcnq1ot1"     
## [1501] "Hsd17b12"      "Slc25a39"      "Plekhj1"       "Ddo"          
## [1505] "Ccs"           "Sumo3"         "Derl1"         "Plau"         
## [1509] "Arhgap5"       "Tpr"           "Ap2b1"         "Nfkbia"       
## [1513] "1110004F10Rik" "Fbxl17"        "Slc7a8"        "Sun1"         
## [1517] "Slc35a1"       "2900052L18Rik" "Napa"          "Dcaf17"       
## [1521] "Eif3a"         "Cstb"          "Hnmt"          "Mlh3"         
## [1525] "Abr"           "Tmem234"       "Prxl2b"        "Kif21a"       
## [1529] "Smarce1"       "Gnpda1"        "Anapc5"        "Mettl27"      
## [1533] "Ppm1a"         "Sh3yl1"        "Jade1"         "Fabp3"        
## [1537] "Hnrnpc"        "Met"           "Stox2"         "Pak1ip1"      
## [1541] "Ptk2"          "Itfg2"         "Rpl36a"        "Mgat4b"       
## [1545] "Ep300"         "Txn2"          "Taldo1"        "Ptprk"        
## [1549] "Ildr1"         "Osbpl9"        "Cmpk1"         "Klf6"         
## [1553] "Cyb5r3"        "Mxi1"          "Nemf"          "Mymx"         
## [1557] "Pde4dip"       "Ptov1"         "Babam2"        "Camta1"       
## [1561] "Foxn3"         "Retreg2"       "Gcsh"          "Igf2r"        
## [1565] "Setd7"         "Dtx3"          "Spc25"         "Psmd11"       
## [1569] "Ppm1g"         "Pcyt2"         "Inpp5j"        "Anapc16"      
## [1573] "Zfp612"        "Ddx17"         "Ranbp2"        "Sf3b2"        
## [1577] "Pdcd4"         "Isoc1"         "Adam10"        "P4hb"         
## [1581] "M6pr"          "Nop53"         "Papss1"        "Fkbp4"        
## [1585] "Pam"           "Echs1"         "Slc48a1"       "Romo1"        
## [1589] "Mrpl34"        "Zbtb38"        "Commd4"        "Zfp871"       
## [1593] "Swt1"          "Ttc39b"        "Imp3"          "Akap11"       
## [1597] "Perp"          "Egln2"         "Pet100"        "Agtrap"       
## [1601] "Ankrd11"       "Hagh"          "Stag2"         "Zfp638"       
## [1605] "Slc44a4"       "Fam98c"        "Npdc1"         "Trappc6b"     
## [1609] "Surf1"         "AI480526"      "Eif3m"         "Fubp1"        
## [1613] "Cetn2"         "Tulp4"         "Arl4a"         "Pcm1"         
## [1617] "Hsbp1"         "Zfp445"        "Ate1"          "Glrx5"        
## [1621] "Unc50"         "Pole4"         "Huwe1"         "Cr1l"         
## [1625] "Prps2"         "Ubr2"          "Dpm1"          "Ogt"          
## [1629] "Rtf1"          "Car2"          "Clk4"          "Clybl"        
## [1633] "Tmem106b"      "Mrpl20"        "Ninj1"         "Myl12b"       
## [1637] "Ogfod3"        "Slc5a3"        "Myl12a"        "Eny2"         
## [1641] "Crip2"         "Mif-ps"        "Larp1b"        "Sgpp2"        
## [1645] "H4c4"          "Hdgfl3"        "Wls"           "Ubn2"         
## [1649] "Manbal"        "Selenoh"       "Naxd"          "Xbp1"         
## [1653] "Usp40"         "Tasor"         "Mif4gd"        "Mapre2"       
## [1657] "Ring1"         "Arl6ip5"       "Atad2b"        "Dnajb6"       
## [1661] "2410006H16Rik" "Mfap1b"        "Map7"          "Tmod3"        
## [1665] "Dnlz"          "Mri1"          "Pfkl"          "Scn4b"        
## [1669] "Zmynd11"       "Ppia"          "Yy1"           "Bpgm"         
## [1673] "Ccdc47"        "Clptm1"        "Phldb2"        "Phf20l1"      
## [1677] "Dctn4"         "Phf14"         "Tomm5"         "Supt4a"       
## [1681] "Rcn2"          "Dhx36"         "Cbx6"          "Bcas2"        
## [1685] "Smc3"          "Caprin1"       "Mysm1"         "Polr2e"       
## [1689] "Slc39a1"       "1810026B05Rik" "Tsc22d1"       "Arpc4"        
## [1693] "Slc25a30"      "Hspb1"         "Ebp"           "Amfr"         
## [1697] "Chchd3"        "Mrps15"        "Rps28"         "Aplp2"        
## [1701] "Blnk"          "Rbm42"         "Gdi1"          "Bod1"         
## [1705] "Smchd1"        "Hook3"         "Rpl24"         "Pld3"         
## [1709] "Wbp2"          "Cyhr1"         "Hoxb5"         "Ensa"         
## [1713] "Lzts2"         "Smad7"         "Gipc2"         "Rab11b"       
## [1717] "Igf1r"         "Snrnp48"       "Rps23-ps2"     "Gstt3"        
## [1721] "Eprs"          "Hnrnpr"        "Gm38394"       "Tuba1b"       
## [1725] "Dnajc10"       "Pim3"          "Abhd16a"       "9530068E07Rik"
## [1729] "Spr"           "Dusp11"        "Tsc22d3"       "Mphosph8"     
## [1733] "Dsp"           "Use1"          "Hist1h2al"     "Itga6"        
## [1737] "Txndc15"       "Pkp4"          "Ndufb9"        "Smarca5"      
## [1741] "Wnk4"          "Gm24270"       "Esf1"          "Cenpb"        
## [1745] "Phip"          "Pbrm1"         "Ndrg2"         "Mesd"         
## [1749] "Cdkn1b"        "Zc3h13"        "Mir6236"       "Gpx4"         
## [1753] "Ndufs2"        "Azin1"         "Septin7"       "CT010467.1"   
## [1757] "Gm37376"       "Ier2"          "Fkbp11"        "Nme7"         
## [1761] "Lars2"         "Gm23935"       "Trpm7"         "Tspan8"       
## [1765] "Atp6v0d1"      "Actb"          "Klk1"          "Wfdc15b"      
## [1769] "Wnk1"
### Cluster 2: MD: Activated (cFos)
### Cluster 3: 
### Cluster 4: EC (Pecam1)
### Cluster 5: CD (Aqp2)
### Cluster 6: IC (Kit)
### Cluster 7: PT (Slc34a1)

FeaturePlot(SO, "Nos1")

VlnPlot(SO, features = "Nos1")

FeaturePlot(SO, "Pappa2")

VlnPlot(SO, features = "Pappa2")

FeaturePlot(SO, "Slc12a1")

VlnPlot(SO, features = "Slc12a1")

FeaturePlot(SO, "Fos")

VlnPlot(SO, features = "Fos")

FeaturePlot(SO, "Pecam1")

VlnPlot(SO, features = "Pecam1")

FeaturePlot(SO, "Aqp2")

VlnPlot(SO, features = "Aqp2")

FeaturePlot(SO, "Kit")

VlnPlot(SO, features = "Kit")

FeaturePlot(SO, "Slc34a1")

VlnPlot(SO, features = "Slc34a1")

2 Filter non-MD Cells and re-cluster

SO2 <- subset(SO, idents = c("4", "5", "6", "7"), invert = TRUE)

DimPlot(SO2)

SO2 <- SCTransform(SO2) %>%
    RunPCA() %>%
    FindNeighbors(dims = 1:30) %>%
    FindClusters() %>%
    RunUMAP(dims = 1:30)
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## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 11529
## Number of edges: 391221
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.7901
## Number of communities: 15
## Elapsed time: 1 seconds
DimPlot(SO2)

markers.to.plot2 <- c("Lrp2",         # PT
                      "Slc5a12",      # PT-S1
                      "Slc13a3",      # PT-S2
                      "Slc16a9",      # PT-S3
                      "Havcr1",       # Injured PT
                      "Epha7",        # dTL
                      "Cryab",        # dTL
                      "Cdh13",        # dTL1
                      "Slc14a2",      # dTL2
                      "Slc12a1",      # TAL
                      "Umod",         # TAL, DCT1
                      "Egf",          # TAL, DCT1,
                      "Cldn10",       # TAL
                      "Cldn16",       # TAL
                      "Nos1",         # MD
                      "Slc12a3",      # DCT
                      "Pvalb",        # DCT1
                      "Slc8a1",       # DCT2, CNT
                      "Aqp2",         # PC
                      "Slc4a1",       # IC-A
                      "Slc26a4",      # IC-B
                      "Nphs1",        # Podo
                      "Ncam1",        # PEC
                      "Flt1",         # Endo
                      "Emcn",         # Glom Endo
                      "Kdr",          # Capillary Endo
                      "Pdgfrb",       # Perivascular
                      "Pdgfra",       # Fib
                      "Piezo2",       # Mesangial
                      "Acta2",        # Mural
                      "Ptprc",        # Immune
                      "Cd74",         # Macrophage
                      "Skap1",        # B/T Cells 
                      "Upk1b",        # Uro
                      "Top2a",         # Proliferation
                      "Cldn5",
                      "Jun",
                      "Fosb"
)
                      
DotPlot(SO2,
features = markers.to.plot2,
dot.scale = 8,
dot.min = 0,
scale.max = 100,
scale.min = 0,
col.min = -2.5,
col.max = 2.5)+
coord_flip()

FeaturePlot(SO2, "Slc12a3")

FeaturePlot(SO2, "Fosb")

FeaturePlot(SO2, "Cldn5")

DimPlot(SO2, group.by = "treatment")

3 Subset and recluster

SO3 <- subset(SO2, idents = c("13"), invert = TRUE)

DimPlot(SO3)

SO3 <- SCTransform(SO3) %>%
    RunPCA() %>%
    FindNeighbors(dims = 1:10) %>%
    FindClusters(resolution = .3) %>%
    RunUMAP(dims = 1:10)
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## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 11458
## Number of edges: 350779
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8595
## Number of communities: 5
## Elapsed time: 1 seconds
DimPlot(SO3)

SO.markers <- FindAllMarkers(SO3, only.pos = TRUE)

SO.markers %>%
    group_by(cluster) %>%
    dplyr::filter(avg_log2FC > .5) %>%
    slice_head(n = 10) %>%
    ungroup() -> top10

DoHeatmap(SO3, features = top10$gene) + NoLegend()

FeaturePlot(SO3, "Nos1")

VlnPlot(SO3, "Nos1", split.by = "treatment")

VlnPlot(SO3, "Nos1", split.by = "sample")

FeaturePlot(SO3, "Pappa2")

VlnPlot(SO3, "Pappa2", split.by = "treatment")

VlnPlot(SO3, "Pappa2", split.by = "sample")

FeaturePlot(SO3, "Atp1a1")

VlnPlot(SO3, "Atp1a1", split.by = "treatment")

VlnPlot(SO3, "Atp1a1", split.by = "sample")

FeaturePlot(SO3, "Cxcl10")

VlnPlot(SO3, "Cxcl10", split.by = "treatment")

VlnPlot(SO3, "Cxcl10", split.by = "sample")

FeaturePlot(SO3, "Cox5b")

VlnPlot(SO3, "Cox5b", split.by = "treatment")

VlnPlot(SO3, "Cox5b", split.by = "sample")

VlnPlot(SO3, "percent.mt", split.by = "treatment")

3.1 Save Object

save(SO3, file = here("outputs", "MD_jwn_v1.rds"))

4 Session Info

sessionInfo()
## R version 4.4.3 (2025-02-28 ucrt)
## Platform: x86_64-w64-mingw32/x64
## Running under: Windows 11 x64 (build 22631)
## 
## Matrix products: default
## 
## 
## locale:
## [1] LC_COLLATE=English_United States.utf8 
## [2] LC_CTYPE=English_United States.utf8   
## [3] LC_MONETARY=English_United States.utf8
## [4] LC_NUMERIC=C                          
## [5] LC_TIME=English_United States.utf8    
## 
## time zone: America/Los_Angeles
## tzcode source: internal
## 
## attached base packages:
## [1] grid      stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] CellChat_2.1.2              igraph_2.1.4               
##  [3] ggtext_0.1.2                ComplexHeatmap_2.22.0      
##  [5] UpSetR_1.4.0                EnhancedVolcano_1.24.0     
##  [7] lubridate_1.9.4             forcats_1.0.0              
##  [9] purrr_1.0.4                 readr_2.1.5                
## [11] tidyr_1.3.1                 tidyverse_2.0.0            
## [13] enrichplot_1.26.6           clusterProfiler_4.14.6     
## [15] gplots_3.2.0                kableExtra_1.4.0           
## [17] ggvenn_0.1.10               data.table_1.17.0          
## [19] readxl_1.4.5                openxlsx_4.2.8             
## [21] car_3.1-3                   carData_3.0-5              
## [23] stringr_1.5.1               here_1.0.1                 
## [25] DESeq2_1.46.0               SummarizedExperiment_1.36.0
## [27] Biobase_2.66.0              MatrixGenerics_1.18.1      
## [29] matrixStats_1.5.0           GenomicRanges_1.58.0       
## [31] GenomeInfoDb_1.42.3         IRanges_2.40.1             
## [33] S4Vectors_0.44.0            BiocGenerics_0.52.0        
## [35] ggrepel_0.9.6               RColorBrewer_1.1-3         
## [37] ggpmisc_0.6.1               ggpp_0.5.8-1               
## [39] tibble_3.2.1                BiocManager_1.30.25        
## [41] ggplot2_3.5.1               knitr_1.50                 
## [43] patchwork_1.3.0             SeuratObject_5.0.2         
## [45] Seurat_4.4.0                dplyr_1.1.4                
## 
## loaded via a namespace (and not attached):
##   [1] R.methodsS3_1.8.2       goftest_1.2-3           Biostrings_2.74.1      
##   [4] vctrs_0.6.5             ggtangle_0.0.6          spatstat.random_3.3-2  
##   [7] digest_0.6.37           png_0.1-8               shape_1.4.6.1          
##  [10] registry_0.5-1          deldir_2.0-4            parallelly_1.42.0      
##  [13] MASS_7.3-64             reshape2_1.4.4          httpuv_1.6.15          
##  [16] foreach_1.5.2           qvalue_2.38.0           withr_3.0.2            
##  [19] ggrastr_1.0.2           xfun_0.51               ggfun_0.1.8            
##  [22] ggpubr_0.6.0            survival_3.8-3          memoise_2.0.1          
##  [25] ggbeeswarm_0.7.2        MatrixModels_0.5-3      gson_0.1.0             
##  [28] systemfonts_1.2.1       tidytree_0.4.6          zoo_1.8-13             
##  [31] GlobalOptions_0.1.2     gtools_3.9.5            pbapply_1.7-2          
##  [34] R.oo_1.27.0             Formula_1.2-5           KEGGREST_1.46.0        
##  [37] promises_1.3.2          httr_1.4.7              rstatix_0.7.2          
##  [40] globals_0.16.3          fitdistrplus_1.2-2      rstudioapi_0.17.1      
##  [43] UCSC.utils_1.2.0        miniUI_0.1.1.1          generics_0.1.3         
##  [46] DOSE_4.0.0              ggalluvial_0.12.5       zlibbioc_1.52.0        
##  [49] polyclip_1.10-7         GenomeInfoDbData_1.2.13 SparseArray_1.6.2      
##  [52] xtable_1.8-4            doParallel_1.0.17       evaluate_1.0.3         
##  [55] S4Arrays_1.6.0          hms_1.1.3               irlba_2.3.5.1          
##  [58] colorspace_2.1-1        polynom_1.4-1           ggnetwork_0.5.13       
##  [61] ROCR_1.0-11             reticulate_1.41.0.1     spatstat.data_3.1-6    
##  [64] magrittr_2.0.3          lmtest_0.9-40           later_1.4.1            
##  [67] ggtree_3.14.0           lattice_0.22-6          spatstat.geom_3.3-5    
##  [70] NMF_0.28                future.apply_1.11.3     SparseM_1.84-2         
##  [73] scattermore_1.2         cowplot_1.1.3           RcppAnnoy_0.0.22       
##  [76] pillar_1.10.1           nlme_3.1-167            iterators_1.0.14       
##  [79] sna_2.8                 gridBase_0.4-7          caTools_1.18.3         
##  [82] compiler_4.4.3          RSpectra_0.16-2         stringi_1.8.4          
##  [85] tensor_1.5              plyr_1.8.9              crayon_1.5.3           
##  [88] abind_1.4-8             gridGraphics_0.5-1      locfit_1.5-9.12        
##  [91] sp_2.2-0                bit_4.6.0               fastmatch_1.1-6        
##  [94] codetools_0.2-20        bslib_0.9.0             GetoptLong_1.0.5       
##  [97] plotly_4.10.4           mime_0.12               splines_4.4.3          
## [100] circlize_0.4.16         Rcpp_1.0.14             quantreg_6.1           
## [103] cellranger_1.1.0        gridtext_0.1.5          blob_1.2.4             
## [106] clue_0.3-66             fs_1.6.5                listenv_0.9.1          
## [109] ggsignif_0.6.4          ggplotify_0.1.2         Matrix_1.7-2           
## [112] tzdb_0.5.0              svglite_2.1.3           pkgconfig_2.0.3        
## [115] network_1.19.0          tools_4.4.3             cachem_1.1.0           
## [118] RSQLite_2.3.9           viridisLite_0.4.2       DBI_1.2.3              
## [121] fastmap_1.2.0           rmarkdown_2.29          scales_1.3.0           
## [124] ica_1.0-3               broom_1.0.7             sass_0.4.9             
## [127] coda_0.19-4.1           FNN_1.1.4.1             dotCall64_1.2          
## [130] RANN_2.6.2              farver_2.1.2            yaml_2.3.10            
## [133] cli_3.6.4               leiden_0.4.3.1          lifecycle_1.0.4        
## [136] uwot_0.2.3              backports_1.5.0         BiocParallel_1.40.0    
## [139] timechange_0.3.0        gtable_0.3.6            rjson_0.2.23           
## [142] ggridges_0.5.6          progressr_0.15.1        parallel_4.4.3         
## [145] ape_5.8-1               jsonlite_1.9.1          bitops_1.0-9           
## [148] bit64_4.6.0-1           Rtsne_0.17              yulab.utils_0.2.0      
## [151] spatstat.utils_3.1-3    BiocNeighbors_2.0.1     zip_2.3.2              
## [154] jquerylib_0.1.4         GOSemSim_2.32.0         spatstat.univar_3.1-2  
## [157] R.utils_2.13.0          lazyeval_0.2.2          shiny_1.10.0           
## [160] htmltools_0.5.8.1       GO.db_3.20.0            sctransform_0.4.1      
## [163] glue_1.8.0              spam_2.11-1             XVector_0.46.0         
## [166] rprojroot_2.0.4         treeio_1.30.0           gridExtra_2.3          
## [169] R6_2.6.1                labeling_0.4.3          cluster_2.1.8          
## [172] rngtools_1.5.2          aplot_0.2.5             statnet.common_4.11.0  
## [175] vipor_0.4.7             DelayedArray_0.32.0     tidyselect_1.2.1       
## [178] xml2_1.3.8              AnnotationDbi_1.68.0    future_1.34.0          
## [181] munsell_0.5.1           KernSmooth_2.23-26      htmlwidgets_1.6.4      
## [184] fgsea_1.32.2            rlang_1.1.5             spatstat.sparse_3.1-0  
## [187] spatstat.explore_3.3-4  beeswarm_0.4.0